I would even be happy with a program that would take a list of *.pak files and create a modsettings.lsx file from it.
That's literally what BG3 Mod Manager (and presumably Vortex) does. It would be nice if BG3 MM (and Vortex) had a native Linux version, but setting it up with Lutris or Bottles isn't that complicated. Bottles is probably easiest for getting the .NET dependencies, but Lutris isn't that difficult either. I used Lutris.
The key thing to getting this working though is once you've got the mod manager installed, you need to symlink your BG3 install folder into the mod manager's prefix, and symlink your BG3's compatdata prefix's "app data" folders to the appropriate place in the mod managers prefix's folders. It sounds more complicated than it actually is. You can do it with a command line, but in Desktop mode you can also use Dolphin:
I browse to where BG3 is installed in ~/.steam/.steam/steamapps/common/ (if your install is on the SD card, the path will be slightly different), and set Dolphin to split view, then on the right-hand side I browse to the BG3 mod manager's prefix, for mine that's ~/Applications/Lutris/prefixes/Baldur's Gate 3 Mod Manager/drive_c/ and from the left-hand "common" side I drag "Baldur's Gate 3" over and drop it in the right-hand "drive_c" side and choose "Link Here" from the context menu that pops up.
Then on the left-hand "common" side I back up to steamapps, then go into compatdata and find the Steam ID for BG3 (1086940) and go into it, [Steam library location]/steamapps/compatdata/1086940/pfx/drive_c/Users/steamuser (or it might be Deck)/AppData/Local/ on the right-hand "drive_c" side now dig into [mod manager prefix location]/drive_c/Users/steamuser (or again, might be Deck)/AppData/Local/ and again drag from the left-hand side anything with Larian Studios or Baldur's Gate 3 in the name, over to the right-hand side and choose "Link Here"
If you use the Script Extender, it also creates a "BG3ScriptExtender" folder in the left-hand side AppData/Local/ folder that you'll need to also drag that over to the right-hand side and "Link Here". If you don't see that folder it's because you haven't run the game with the Script Extender installed yet.
Why all the linking back and forth? Because Wine and Proton install Windows apps in their own separate sandboxed environments. Each app sees it's own C drive, and not any other app's C drive. So in this case it would be as if Baldur's Gate 3 is installed on your desktop, while BG3 Mod Manager is installed on your laptop, they're both installed but they don't see or talk to each other in any way. Two separate systems. By symlinking the folders we're letting the BG3 Mod Manager see the game install and its appdata folders as if they were installed in it's own unique sandbox.